The bulk of the paper was devoted to three main criticisms of Smith: The opinion that Smith had once been a true prophet, but had fallen by advocating polygamy, Exaltation, and other controversial doctrines; the opinion that Smith, as both Mayor of Nauvoo and President of the Church held too much power, which was further consolidated by the overwhelmingly Mormon make-up of Nauvoo's courts and city council, who intended establishing a theocracy via the Council of Fifty; and the belief that Smith had corrupted women by forcing, coercing or introducing them into plural marriage.

In response to public outrage generated by the paper, the Nauvoo city council passed an ordinance declaring the newspaper a public nuisance designed to promote violence against Smith and his followers. They reached this decision after lengthy discussion, including citation of William Blackstone's legal canon, which included a libelous press as a public nuisance. According to the council's minutes, Smith said he "...would rather die tomorrow and have the thing smashed, than live and have it go on, for it was exciting the spirit of mobocracy among the people, and bringing death and destruction upon us.

Under the council's new ordinance, Smith, as Nauvoo's mayor, in conjunction with the city council, ordered the city marshal to destroy the paper and the press on June 10, 1844. By the city marshal's account, the destruction of the press type was carried out orderly and peaceably. However, Charles A. Foster, a co-publisher of the Expositor, reported on June 12 that additionally to the printing press being destroyed, the group which he dubbed "several hundred minions ... injured the building very materially" as well, though this is contradicted by the fact that the building was in use for at least another decade.

Smith’s critics said that he had violated freedom of the press. Some sought legal charges against Smith for the destruction of the press, including charges of inciting riot and treason. Violent threats were made against Smith and the Mormon community. Thomas Sharp, editor of the Warsaw Signal, a newspaper hostile to the Mormons, editorialized:

War and extermination is inevitable! Citizens ARISE, ONE and ALL!!!—Can you stand by, and suffer such INFERNAL DEVILS! To ROB men of their property and RIGHTS, without avenging them. We have no time for comment, every man will make his own. LET IT BE MADE WITH POWDER AND BALL!!! (Warsaw Signal, 12 June1844, p. 2.)

Warrants from outside Nauvoo were brought in against Smith and dismissed in Nauvoo courts on a writ of habeas corpus. Smith declared martial law on June 18 and called out the Nauvoo Legion, an organized city militia of about 5,000 men, to protect Nauvoo from outside violence.

Incarceration at Carthage Jail

Illinois Governor Thomas Ford proposed a trial by a non-Mormon jury in Carthage, the county seat, and guaranteed Smith's safety. Smith originally planned on leaving rather than surrendering but when criticized by some followers is reported to have said "If my life is of no value to my friends it is of none to myself. Smith reluctantly agreed and submitted to arrest, further quoted as saying "I am going like a lamb to the slaughter; but I am calm as a summer’s morning; I have a conscience void of offense towards God, and towards all men. I shall die innocent, and it shall yet be said of me — he was murdered in cold blood.

On 25 June1844, Joseph and Hyrum Smith, along with the other fifteen city council members and some friends, surrendered to Carthage constableWilliam Bettisworth on the original charge of riot. Almost immediately Joseph and Hyrum were charged with treason against the state of Illinois for declaring martial law in Nauvoo, by a warrant founded upon the oaths of A. O. Norton and Augustine Spencer. At a preliminary hearing that afternoon the city council members were released on $500 bonds, pending later trial. The judge ordered Joseph and Hyrum Smith to be held in jail until they could be tried for treason, a capital offense.

Attack by the mob

Before a trial could be held, a mob of about 200 armed men, their faces painted black with wet gunpowder, stormed the jail in the late afternoon of 27 June1844. As the mob was approaching, the jailer became nervous, and informed Smith of the group. In a letter dated 10 July1844, one of the jailers wrote that Smith, expecting the Nauvoo Legion, said "Don't trouble yourself ... they've come to rescue me." Smith was unaware that Jonathan Dunham, major general of the Nauvoo Legion, had not dispatched the unit to Carthage to protect him. Allen Joseph Stout contended that by remaining inactive, Dunham had violated an official order written by Smith after he had been jailed in Carthage.

The Carthage Greys reportedly feigned defense of the jail by firing shots or blanks over the attackers' heads, and some of the Greys reportedly joined the mob, who rushed up the stairs.

The mob fired shots through the door and attempted to push the door open to fire into the room. Hyrum Smith was shot in the face, just to the left of his nose. He cried out, "I am a dead man!" and collapsed. His body received five additional gunshot wounds.

Smith, Taylor, and Richards attempted to defend themselves. Taylor and Richards attempted to use walking sticks in order to deflect the guns as they were thrust inside the cell, from behind the door. Smith used a small pepper-box pistol that Cyrus Wheelock had given him when Wheelock had visited the jail earlier that day. Three of the six barrels misfired. Taylor later stated he had been informed that two assailants had died of wounds received from the pistol; however, witnesses identified three injured men who survived and were later indicted for the murder of Joseph Smith.

John Taylor was shot four or five times and was severely injured, but survived, one shot being stopped by his pocket watch (the hands stopped at 5:16). Richards escaped unscathed as he was pushed behind the door when it was forced open.

Joseph Smith made his way towards the window. As he prepared to jump down, Richards reported that he was shot twice in the back and a third bullet, fired from a musket on the ground outside, hit him in the chest.

Taylor and Richards' accounts both report that as Smith fell from the window, he called out "Oh Lord, my God!". Some have alleged that the context of this statement was an attempt by Joseph Smith to use a Masonic distress signal.

There are varying accounts of what happened next. Taylor and Richards' accounts state that Smith was dead when he landed after his fall. One eyewitness, William Daniels, wrote in his 1845 account that Smith was alive when mob members propped his body against a nearby well, assembled a makeshift firing squad, and shot him before fleeing. Daniels' account also states that one man tried to decapitate Smith for a bounty, but was prevented by divine intervention. There were additional reports that thunder and lightning frightened the mob off. Mob members fled, shouting, "The Mormons are coming," although there was no such force nearby.

"My sons were thrown into jail, where they remained in company with Brothers Richards, Taylor and Markham. At the end of this time, the Governor disbanded most of the men, but left a guard of eight of our bitterest enemies over the jail, and sixty more of the same character about a hundred yards distant. He then came into Nauvoo with a guard of fifty or sixty men, made a short speech, and returned immediately. During his absence from Carthage, the guard rushed Brother Markham out of the place at the point of the bayonet. Soon after this two hundred of those discharged in the morning rushed into Carthage, armed and painted black, red and yellow, and in ten minutes fled again, leaving my sons' murdered and mangled corpses!"

After the deaths, much speculation was made about who was responsible. Governor Ford was accused of knowing about the plot to kill Smith, and some said he even approved of it. Ford denied this, but he later wrote that it was good for the Mormons to have been driven out of the state and said that their beliefs and actions were too different to have survived in Illinois. He said Smith was "the most successful impostor in modern times," and that some people "expect more protection from the laws than the laws are able to furnish in the face of popular excitement."

Taylor statement concerning Joseph Smith's shots

John Taylor, who became the third President of the Church of Jesus Christ of Latter-day Saints, made these statements concerning the death of Joseph Smith:

"Elder Cyrus H. Wheelock came in to see us, and when he was about leaving drew a small pistol, a six-shooter, from his pocket, remarking at the same time, 'Would any of you like to have this?' Brother Joseph immediately replied, 'Yes, give it to me,' whereupon he took the pistol, and put it in his pantaloons pocket.... I was sitting at one of the front windows of the jail, when I saw a number of men, with painted faces, coming around the corner of the jail, and aiming towards the stairs.... (Hyrum was shot in the face and was killed instantly, John Taylor continued)

I shall never forget the deep feeling of sympathy and regard manifested in the countenance of Brother Joseph as he drew nigh to Hyrum, and, leaning over him, exclaimed, 'Oh! my poor, dear brother Hyrum!' He, however, instantly arose, and with a firm, quick step, and a determined expression of countenance, approached the door, and pulling the six-shooter left by Brother Wheelock from his pocket, opened the door slightly, and snapped the pistol six successive times; only three of the barrels, however, were discharged. I afterwards understood that two or three were wounded by these discharges, two of whom, I am informed died." (History of the Church, Vol. 7, p. 100, 102 & 103)"

Taylor's statement evidences that there was discussion regarding the possible death of two men, but it was hearsay on Taylor's part.

"Most accounts seem to agree that three mob members were wounded by Joseph’s gunfire: John Wills, an Irishman who had joined the mob from “his congenital love of a brawl,” was apparently shot in the arm by the prophet (CHC 2:285 n.19); William Voras, a “half grown, hobbledehoy from Bear Creek,” was shot in the shoulder by Joseph (ibid.); and William Gallaher, a “southerner from the Mississippi Bottom” who supposedly was shot in the face. (Ibid., see also Oaks and Hill, 52.) A Mr. John Hay claimed that a fourth man “‘whose name I will not mention, as he is prepared to prove an alibi, and besides stands six feet two in his moccasins’” was also wounded (CHC 2:285 n.19.) This fourth man was identified as a Mr. Allen, who, along with Wills, Voras and Gallaher, were all indicted for the murder of Joseph and Hyrum. Wills, Voras and Gallaher “were probably named in the indictment because of their wounds, which testimony showed were received at the jail, were irrefutable evidence that they had participated in the mob.” (Oaks and Hill, 52.) According to one source, the “citizens of Green Plains were said to have given Gallaher and Voras new suits of clothes for their parts in the killing.” (Ibid., 53.) None of these four assailants were ever arrested or appeared for trial, and one report claimed that at least three of these men had left the state. (Ibid., 79.)

Although it is possible that one or more of these men died as a result of the wounds they received during their mob attack, there is no evidence to suggest that such is the case, other than second or third hand reports which most scholars have dismissed as folklore."

Interment

Joseph and Hyrum Smith's bodies were returned to Nauvoo the next day. The bodies were cleaned and examined, and death masks were made, preserving their facial features and structures.

A public viewing was held on 29 June1844, after which empty coffins weighted with sandbags were used at the public burial. (This was done to prevent theft or mutilation of the bodies.) The actual coffins bearing the bodies of the Smith brothers were initially buried under the unfinished Nauvoo House, then disinterred and deeply reburied under an out-building on the Smith homestead. The exact location of the grave site was soon lost to memory.

In 1928 Frederick M. Smith, president of the Reorganized Church of Jesus Christ of Latter Day Saints and grandson of Joseph Smith, fearing that rising water from the Mississippi River would destroy the grave site, authorized civil engineer William O. Hands to conduct an excavation to find Joseph and Hyrum's bodies. Hands conducted extensive digging on the Smith homestead, and located the bodies, as well as finding the remains of Joseph's wife, Emma, which had been buried in the same place. The remains—which were badly decomposed—were examined and photographed, and the bodies were reinterred.